BIOCOMPLEXITY: Hexapod Phylogenomics - Bringing Phylogenetic Supercomputing to the Masses

生物复杂性：六足体系统发育组学 - 将系统发育超级计算带给大众

• 批准号: 0120718
• 负责人: Michael Whiting
• 金额: $ 134万
• 依托单位: Brigham Young University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-01-01 至 2006-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0120718&HistoricalAwards=false
• 关键词: BIOCOMPLEXITY; Hexapod; Phylogenomics; Bringing; Phylogenetic

0120718WhitingA Biocomplexity in the Environment: Genome-Enabled grant has been awarded to an interdisciplinary team of researchers at the Brigham Young University that combines expertise in computer science, statistics, and phylogenetic systematics to address three fundamental questions in evolutionary biology, genomics, and computational biology. (1) What are the major relationships among Hexapods (insects and related taxa)? (2) How has mitochondrial genome evolution occurred relative to Hexapod diversity? (3) How can we develop fast, parallel computer algorithms to reconstruct phylogenetic relationships for large data sets? To answer these questions, the investigators will sequence about 2500 species across hexapod diversity for about 12 nuclear genes representing a total sequencing effort of 30 million base pairs. They will then sequence about 120 mitochondrial genomes across the major lineages representing each of the hexapod orders to examine mitochondrial genome evolution in the context of a well established phylogeny from the 12 nuclear genes. This represents another 1.8 million nucleotides of sequence. Parallel-processing algorithms will be developed for computational analysis of large nucleotide sequence data sets. The results will provide a framework for understanding Hexapod diversity (crucial for understanding agricultural pests, disease vectors, etc.), mitochondrial genome evolution (instrumental in understanding the functional significance of gene rearrangements), and easily available parallel approaches for phylogenetics. Because phylogenetics is becoming an instrumental tool in the study of human disease (both due to infection and the genetic component of complex diseases such as cancer and coronary artery disease), the ability to reconstruct phylogenetic relationships accurately and with great speed for ever-increasing data sets is key to making the link between genetic changes and disease risk factors. The investigators will heavily involve undergraduates, graduate students, and postdoctoral fellows in every phase of this work and provide outlets in the form of publications and informational websites.DEB-0120719Michael Whiting, Keith Crandall, Mark Clement, Quin Snell, David WhitingA grant has been awarded to an interdisciplinary team of researchers at the Brigham Young University that combines expertise in computer science, statistics, and phylogenetic systematics to address three fundamental questions in evolutionary biology, genomics, and computational biology: 1) What are the major relationships among Hexapods (insects and related taxa)? 2) How has mitochondrial genome evolution occurred relative to Hexapod diversity? And 3) how can we develop fast, parallel computer algorithms to reconstruct phylogenetic relationships for large data sets? To answer these questions, the investigators will sequence ~2500 species across hexapod diversity for ~12 genes representing a total sequencing effort of 30 million base pairs. They will then sequence ~120 mitochondrial genomes across the major lineages representing each of the hexapod orders to examine mitochondrial genome evolution in the context of our well established phylogeny from the 12 nuclear genes. This represents another 1.8 million nucleotides of sequence. Finally we will develop parallel algorithms for computational analysis of nucleotide sequence data. The results will provide a framework for understanding Hexapod diversity (crucial for understanding agricultural pests, disease vectors, etc.), mitochondrial genome evolution (instrumental in understanding the functional significance of gene rearrangements), and easily available parallel approaches for phylogenetics. Since phylogenetics is becoming an instrumental tool in the study of human disease (both due to infection and the genetic component of complex diseases such as cancer and coronary artery disease), the ability to reconstruct phylogenetic relationships accurately and with great speed for ever-increasing data sets is key to making the link between genetic changes and disease risk factors. The investigators will heavily involve undergraduates, graduate students, and postdoctoral fellows in every phase of this work and provide outlets in the form of publications and informational websites.

0120718 WhitingA环境中的生物复杂性：基因组启用补助金已授予杨百翰大学的跨学科研究团队，该团队结合了计算机科学，统计学和系统发育系统学的专业知识，以解决进化生物学，基因组学和计算生物学中的三个基本问题。(1)六足动物（昆虫和相关类群）之间的主要关系是什么？(2)线粒体基因组进化相对于六足动物多样性是如何发生的？ (3)我们如何开发快速、并行的计算机算法来重建大型数据集的系统发育关系？ 为了回答这些问题，研究人员将对大约2500种六足动物多样性的大约12个核基因进行测序，总共测序工作量为3000万个碱基对。 然后，他们将对代表每一个六足目的主要谱系中的大约120个线粒体基因组进行测序，以在12个核基因的成熟的同源性背景下研究线粒体基因组的进化。 这代表了另外180万个核苷酸的序列。 将开发用于大型核苷酸序列数据集的计算分析的序列处理算法。 研究结果将为理解六足动物多样性提供一个框架（对于理解农业害虫、病媒等至关重要），线粒体基因组进化（有助于理解基因重排的功能意义），以及容易获得的平行方法用于线粒体遗传学。 由于系统发育遗传学正在成为研究人类疾病（由于感染和复杂疾病的遗传成分，如癌症和冠状动脉疾病）的工具，因此能够准确地重建系统发育关系，并快速获得不断增加的数据集是将遗传变化与疾病风险因素联系起来的关键。 研究人员将在这项工作的每一个阶段都大量涉及本科生、研究生和博士后研究员，并以出版物和信息网站的形式提供出路。DEB-0120719迈克尔·怀汀、基思·克兰德尔、马克·克莱门特、奎因·斯内尔、大卫·怀汀杨百翰大学的一个跨学科研究小组获得了一笔赠款，该小组将计算机科学、统计学、和系统发生系统学来解决进化生物学，基因组学和计算生物学中的三个基本问题：1）六足动物（昆虫和相关类群）之间的主要关系是什么？2)线粒体基因组进化相对于六足动物多样性是如何发生的？ 以及3）我们如何开发快速，并行的计算机算法来重建大数据集的系统发育关系？ 为了回答这些问题，研究人员将对六足动物多样性中的约2500个物种的约12个基因进行测序，这代表了3000万个碱基对的测序工作。 然后，他们将对代表每一个六足目的主要谱系中的约120个线粒体基因组进行测序，以在我们从12个核基因中确定的同源性的背景下研究线粒体基因组的进化。 这代表了另外180万个核苷酸的序列。 最后，我们将开发用于核苷酸序列数据的计算分析的并行算法。 研究结果将为理解六足动物多样性提供一个框架（对于理解农业害虫、病媒等至关重要），线粒体基因组进化（有助于理解基因重排的功能意义），以及容易获得的平行方法用于线粒体遗传学。 由于系统发育遗传学正在成为研究人类疾病（由于感染和复杂疾病的遗传成分，如癌症和冠状动脉疾病）的工具，因此能够准确地重建系统发育关系，并快速获得不断增加的数据集是将遗传变化与疾病风险因素联系起来的关键。 研究人员将在这项工作的每一个阶段大量参与本科生，研究生和博士后研究员，并以出版物和信息网站的形式提供渠道。